201
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He W, Crawford MJ, Rapireddy S, Madrid M, Gil RR, Ly DH, Achim C. The structure of a gamma-modified peptide nucleic acid duplex. MOLECULAR BIOSYSTEMS 2010; 6:1619-29. [PMID: 20386807 DOI: 10.1039/c002254c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper presents the results of an NMR spectroscopy and distance-restrained molecular dynamics (MD) study of a gamma-methylated, palindromic, 8-base pair peptide nucleic acid (gamma-PNA) duplex. The goal of this study was to examine the impact of the gamma-backbone modification on the structure of the PNA duplex. The 2D NMR information involving the backbone methyl group, especially the NOEs between the methyl protons and those of the amide and methylene groups of the backbone, led to distance restraints useful in the elucidation of the structure of the backbone of gamma-PNA. Integration of the NOE peaks resulted in 138 inter-proton distance restraints, which were used in ten independent simulated annealing followed by 2 ns restrained MD runs. These simulations led to the conclusion that the gamma-PNA duplex adopts a general P-form helical structure similar to that observed for non-modified PNA but with a smaller base pair rise, which is an A-like helical feature, and a slight helical bending towards the major groove (PDB ID ). These properties of the gamma-PNA duplex may be induced by the gamma-methyl group. A similar effect of the methyl group was revealed by a previous NMR study of single stranded gamma-PNA [A. Dragulescu-Andrasi, S. Rapireddy, B. M. Frezza, C. Gayathri, R. R. Gil and D. H. Ly, J. Am. Chem. Soc., 2006, 128, 10258-10267]. It appears that the steric constraint exerted by the gamma-methyl on the backbone orientation is relatively independent of the base pairing and stacking and thus is likely to manifest when other substituents are introduced at the gamma-position of the PNA.
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Affiliation(s)
- Wei He
- Department of Chemistry, Carnegie Mellon University, 4400 5th Avenue, Pittsburgh, PA 15213, USA
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202
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Lusvarghi S, Murphy CT, Roy S, Tanious FA, Sacui I, Wilson WD, Ly DH, Armitage BA. Loop and backbone modifications of peptide nucleic acid improve g-quadruplex binding selectivity. J Am Chem Soc 2010; 131:18415-24. [PMID: 19947597 DOI: 10.1021/ja907250j] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Targeting guanine (G) quadruplex structures is an exciting new strategy with potential for controlling gene expression and designing anticancer agents. Guanine-rich peptide nucleic acid (PNA) oligomers bind to homologous DNA and RNA to form hetero-G-quadruplexes but can also bind to complementary cytosine-rich sequences to form heteroduplexes. In this study, we incorporated backbone modifications into G-rich PNAs to improve the selectivity for quadruplex versus duplex formation. Incorporation of abasic sites as well as chiral modifications to the backbone were found to be effective strategies for improving selectivity as shown by UV-melting and surface plasmon resonance measurements. The enhanced selectivity is due primarily to decreased affinity for complementary sequences, since binding to the homologous DNA to form PNA-DNA heteroquadruplexes retains high affinity. The improved selectivity of these PNAs is an important step toward using PNAs for regulating gene expression by G-quadruplex formation.
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Affiliation(s)
- Sabrina Lusvarghi
- Departments of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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203
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Ishizuka T, Tedeschi T, Corradini R, Komiyama M, Sforza S, Marchelli R. SSB-assisted duplex invasion of preorganized PNA into double-stranded DNA. Chembiochem 2010; 10:2607-12. [PMID: 19760691 DOI: 10.1002/cbic.200900381] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Takumi Ishizuka
- Department of Organic and Industrial Chemistry, University of Parma, Viale G. P. Usberti 17/a, University Campus, Parma, 43100, Italy
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204
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Lu XW, Zeng Y, Liu CF. Modulating the hybridization property of PNA with a peptoid-like side chain. Org Lett 2009; 11:2329-32. [PMID: 19438197 DOI: 10.1021/ol900587b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modification on the gamma-N of the PNA backbone yielded a PNA analogue with a peptoid-like side chain. We found that the length of the side chain was important in influencing the hybridization affinity of the modified PNA.
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Affiliation(s)
- Xiao-Wei Lu
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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205
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Sahu B, Chenna V, Lathrop KL, Thomas SM, Zon G, Livak KJ, Ly DH. Synthesis of conformationally preorganized and cell-permeable guanidine-based gamma-peptide nucleic acids (gammaGPNAs). J Org Chem 2009; 74:1509-16. [PMID: 19161276 PMCID: PMC2650244 DOI: 10.1021/jo802211n] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A general method for preparing optically pure guanidine-based gamma-peptide nucleic acid (gammaGPNA) monomers for all four natural nucleobases (A, C, G, and T) is described. These second-generation gammaGPNAs differ from the first-generation GPNAs in that the guanidinium group is installed at the gamma- instead of the alpha-position of the N-(2-aminoethyl)glycine backbone unit. This positional switch enables GPNAs to be synthesized from relatively cheap L- as opposed to D-amino acids. Unlike their alpha-predecessors, which are randomly folded, gammaGPNAs prepared from L-amino acids are preorganized into a right-handed helix and bind to DNA and RNA with exceptionally high affinity and sequence selectivity and are readily taken up by mammalian cells.
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Affiliation(s)
- Bichismita Sahu
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Venugopal Chenna
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Kira L. Lathrop
- Eye and Ear Institute, University of Pittsburgh, 203 Lothrop Street, Pittsburgh, Pennsylvania 15261
| | - Sufi M. Thomas
- Department of Otolaryngology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, Pennsylvania 15213 and
| | - Gerald Zon
- Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404
| | - Kenneth J. Livak
- Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
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206
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Totsingan F, Tedeschi T, Sforza S, Corradini R, Marchelli R. Highly selective single nucleotide polymorphism recognition by a chiral (5S) PNA beacon. Chirality 2009; 21:245-53. [PMID: 18853465 DOI: 10.1002/chir.20659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A chiral peptide nucleic acid (PNA) beacon containing a C-5 modified monomer based on L-lysine was synthesized. The terminal amino group of the lysine side chain was linked to a spacer for future applications on surfaces. The PNA beacon bears a carboxyfluorescein fluorophore and a dabcyl quencher at opposite ends. The DNA binding properties were compared with those of a homologous PNA beacon containing only achiral monomers. Both beacons underwent a fluorescence increase in the presence of complementary DNA, with higher efficiency and higher selectivity (evaluated using single mismatched DNA sequences) observed for the chiral monomer containing PNA. Ion exchange (IE) HPLC with fluorimetric detection was used in combination with the beacon for the selective detection of complementary DNA. A fluorescent peak corresponding to the PNA beacon:DNA duplex was observed at a very low detection limit (1 nM). The discriminating capacity of the chiral PNA beacon for a single mismatch was found to be superior to those observed with the unmodified one, thus confirming the potency of chirality for increasing the affinity and specificity of DNA recognition.
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Affiliation(s)
- Filbert Totsingan
- Dipartimento di Chimica Organica e Industriale Università di Parma, 43100 Parma, Italy
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207
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Schlegel M, Xie X, Zhang L, Meggers E. Insight into the High Duplex Stability of the Simplified Nucleic Acid GNA. Angew Chem Int Ed Engl 2009; 48:960-3. [DOI: 10.1002/anie.200803472] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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208
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Schlegel M, Xie X, Zhang L, Meggers E. Insight into the High Duplex Stability of the Simplified Nucleic Acid GNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200803472] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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209
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Chenna V, Rapireddy S, Sahu B, Ausin C, Pedroso E, Ly DH. A simple cytosine to G-clamp nucleobase substitution enables chiral gamma-PNAs to invade mixed-sequence double-helical B-form DNA. Chembiochem 2008; 9:2388-91. [PMID: 18816545 DOI: 10.1002/cbic.200800441] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Venugopal Chenna
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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210
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Pensato S, Domenico D'Andrea L, Pedone C, Romanelli A. New Synthetic Route to γ-Mercaptomethyl PNA Monomers. SYNTHETIC COMMUN 2008. [DOI: 10.1080/00397910802219122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Soccorsa Pensato
- a University of Naples “Federico II,” Department of Biological Science , School of Biotechnological Sciences , Napoli, Italy
| | | | - Carlo Pedone
- a University of Naples “Federico II,” Department of Biological Science , School of Biotechnological Sciences , Napoli, Italy
| | - Alessandra Romanelli
- a University of Naples “Federico II,” Department of Biological Science , School of Biotechnological Sciences , Napoli, Italy
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211
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Kleiner RE, Brudno Y, Birnbaum ME, Liu DR. DNA-templated polymerization of side-chain-functionalized peptide nucleic acid aldehydes. J Am Chem Soc 2008; 130:4646-59. [PMID: 18341334 PMCID: PMC2748799 DOI: 10.1021/ja0753997] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA-templated polymerization of synthetic building blocks provides a potential route to the laboratory evolution of sequence-defined polymers with structures and properties not necessarily limited to those of natural biopolymers. We previously reported the efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid (PNA) aldehydes. Here, we report the enzyme-free, DNA-templated polymerization of side-chain-functionalized PNA tetramer and pentamer aldehydes. We observed that polymerization of tetramer and pentamer PNA building blocks with a single lysine-based side chain at various positions in the building block could proceed efficiently and sequence specifically. In addition, DNA-templated polymerization also proceeded efficiently and in a sequence-specific manner with pentamer PNA aldehydes containing two or three lysine side chains in a single building block to generate more densely functionalized polymers. To further our understanding of side-chain compatibility and expand the capabilities of this system, we also examined the polymerization efficiencies of 20 pentamer building blocks each containing one of five different side-chain groups and four different side-chain regio- and stereochemistries. Polymerization reactions were efficient for all five different side-chain groups and for three of the four combinations of side-chain regio- and stereochemistries. Differences in the efficiency and initial rate of polymerization correlate with the apparent melting temperature of each building block, which is dependent on side-chain regio- and stereochemistry but relatively insensitive to side-chain structure among the substrates tested. Our findings represent a significant step toward the evolution of sequence-defined synthetic polymers and also demonstrate that enzyme-free nucleic acid-templated polymerization can occur efficiently using substrates with a wide range of side-chain structures, functionalization positions within each building block, and functionalization densities.
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Affiliation(s)
- Ralph E. Kleiner
- Contribution from the Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Yevgeny Brudno
- Contribution from the Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Michael E. Birnbaum
- Contribution from the Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - David R. Liu
- Contribution from the Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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212
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Moggio L, Romanelli A, Gambari R, Bianchi N, Borgatti M, Fabbri E, Mancini I, di Blasio B, Pedone C, Messere A. Alternate PNA-DNA chimeras (PNA-DNA)(n): synthesis, binding properties and biological activity. Biopolymers 2008; 88:815-22. [PMID: 17918186 DOI: 10.1002/bip.20857] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Peptide nucleic acids (PNAs) are oligonucleotide mimics in which the sugar-phosphate backbone has been replaced by a pseudo-peptide backbone. Among PNA-based molecules, PNA-DNA conjugates characterized by tracts of DNA bound to N and/or C terminus of PNA are very soluble in aqueous media, are able to recognize exclusively single strands of DNA and RNA in antiparallel fashion, activate RNAse H, bind to transcription factors and are more stable than DNA to nucleases degradation. Very little information is available on chimeras constituted of alternating monomers of PNA and DNA. In this article, we describe a simple fully automated strategy for the synthesis of 6-mer and 10-mer alternate PNA-DNA chimeras consisting of polythymine oligomers, stability assays in fetal calf serum, UV and CD studies of the single strand alternate chimeras and of alternate chimera/DNA and alternate chimera/RNA duplexes. Evidences supporting the formation of duplex hybrids were found. Furthermore, the ability of forming Hoogsteen base pairing with duplex DNA was investigated. Finally, we tested the ability of the PNA-DNA alternates in (a) interfering with reverse transcription of eukaryotic mRNA and (b) inhibiting DNA-protein interactions.
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Affiliation(s)
- Loredana Moggio
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy
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213
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Sforza S, Tedeschi T, Corradini R, Marchelli R. Induction of Helical Handedness and DNA Binding Properties of Peptide Nucleic Acids (PNAs) with Two Stereogenic Centres. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700644] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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214
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Berni E, Kauffmann B, Bao C, Lefeuvre J, Bassani DM, Huc I. Assessing the Mechanical Properties of a Molecular Spring. Chemistry 2007; 13:8463-9. [PMID: 17661324 DOI: 10.1002/chem.200700847] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report on the dramatic effect of increasing helix diameter on the hybridization of oligopyridine-dicarboxamide strands into double helices. Upon replacing a single pyridine by a 1,8-diazaanthracene unit within an oligomeric strand, a 4.7 A enlargement of the helix diameter occurs parallel to the long anthracene axis. This structure change results in a spectacular stabilization of the double helical hybrids derived from these strands (factors of over 10(7)). Detailed investigations of the hybridization process using X-ray crystallography, NMR, fluorescence measurements and molecular mechanics calculations allowed us to assign the duplex stabilization to two enthalpic effects. First, the increase in diameter results in an augmented surface, involved in intermolecular pi-pi stacking. Second, the enlarged diameter leads to a lower tilt angle of the helical strand, with respect to the helix axis, which in turn results in smaller dihedral angles at the aryl-amide linkages and thus a considerably lowered enthalpic cost of the spring-like extension of the strands during the hybridization process. These results provide novel insights into how subtle tuning of molecular components may result in considerable and rationalizable changes in double helical supramolecular architectures.
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Affiliation(s)
- Emanuela Berni
- Université Bordeaux 1 - ENITAB - CNRS UMR5248, Institut Européen, de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France
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215
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Pensato S, Saviano M, Romanelli A. New peptide nucleic acid analogues: synthesis and applications. Expert Opin Biol Ther 2007; 7:1219-32. [PMID: 17696820 DOI: 10.1517/14712598.7.8.1219] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Peptide nucleic acids are oligonucleotide mimics characterised by high chemical and enzymatic stability, high specificity and affinity toward complementary DNA/RNA. The lack of charge and polar groups in the backbone decrease their solubility in aqueous environment and their ability to cross cell membranes, reducing their performance in in vivo applications. To improve solubility, increase affinity and specificity of binding and to control recognition between nucleic acids, several analogues bearing modifications on the nucleobase, nucleobase-backbone linker and on the backbone were synthesised. This paper describes the synthesis and applications of Peptide nucleic acid analogues and discusses the potential of analogues for which no application is reported.
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Affiliation(s)
- Soccorsa Pensato
- Università degli Studi di Napoli Federico II, Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Napoli, Italy
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216
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Corradini R, Sforza S, Tedeschi T, Marchelli R. Chirality as a tool in nucleic acid recognition: principles and relevance in biotechnology and in medicinal chemistry. Chirality 2007; 19:269-94. [PMID: 17345563 DOI: 10.1002/chir.20372] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The understanding of the interaction of chiral species with DNA or RNA is very important for the development of new tools in biology and of new drugs. Several cases in which chirality is a crucial point in determining the DNA binding mode are reviewed and discussed, with the aim of illustrating how chirality can be considered as a tool for improving the understanding of mechanisms and the effectiveness of nucleic acid recognition. The review is divided into two parts: the former describes examples of chiral species interacting with DNA: intercalators, metal complexes, and groove binders; the latter part is dedicated to chirality in DNA analogs, with discussion of phosphate stereochemistry and chirality of ribose substitutes, in particular of peptide nucleic acids (PNAs) for which a number of works have been published recently dealing with the effect of chirality in DNA recognition. The discussion is intended to show how enantiomeric recognition originates at the molecular level, by exploiting the enormous progresses recently achieved in the field of structural characterization of complexes formed by nucleic acid with their ligands by crystallographic and spectroscopic methods. Examples of application of the DNA binding molecules described and the role of chirality in DNA recognition relevant for biotechnology or medicinal chemistry are reported.
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Affiliation(s)
- Roberto Corradini
- Dipartimento di Chimica Organica e Industriale, Università di Parma, I-4310 Parma, Italy.
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217
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Englund EA, Appella DH. Gamma-substituted peptide nucleic acids constructed from L-lysine are a versatile scaffold for multifunctional display. Angew Chem Int Ed Engl 2007; 46:1414-8. [PMID: 17133633 DOI: 10.1002/anie.200603483] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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218
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Englund E, Appella D. γ-Substituted Peptide Nucleic Acids Constructed fromL-Lysine are a Versatile Scaffold for Multifunctional Display. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603483] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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219
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